Land drainage can have negative side effects, such as: the increasing of drought hazard in rain-fed agriculture during dry spells; the decomposition of organic matter in the soil; the disappearance of peats through oxidation upon exposure to air and sunshine; the formation of acids in potentially acid sulphate soils; and the impoverishment of indigenous flora and fauna. The negative effects of land drainage usually owe their source to adverse soil conditions in the area being drained; pollution of drainage water is usually caused by other activities in the area, such as over-fertilization, the application of chemicals, or the use of poor-quality irrigation water. If the water being discharged through the drain is polluted by elements leached from the soil, this can have a harmful effect on the environment. The polluting elements may be fertilizers, toxic chemicals, salts, or acids. These may severely affect the quality of the water, or even render it unfit for further use, and cause the ecosystem to be gravely disturbed. Land drainage as such in areas prone to inundation is mostly an improper measure, as it creates new pathways for the water and may thus strengthen the inundations and cause additional erosion.
Drainage has long been regarded by many decision-makers as a step towards national prosperity because of the increase in agricultural land and the control of flooding. The examples of the unforeseen results of drainage are found in almost every river system of Europe, and in many cases the ill-effects are still accumulating, since the cure to one problem is often the cause of several more.